Basics of EXAFS

Processing
Shelly Kelly
2009 UOP LLC. All rights reserved.
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File Number
X-ray-Absorption Fine Structure
Attenuation of x-rays
I
t
= I
0
e
-(E)x
Absorption coefficient
(E) I
f
/I
0
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File Number
X-ray-Absorption Fine Structure
R
0
Photoelectron
Scattered
Photoelectron
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Fourier Transform of (k)
Similar to an atomic radial distribution function
- Distance
- Number
- Type
- Structural disorder
Fourier transform is not a radial distribution function
- See http://www.xafs.org/Common_Mistakes
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File Number
Outline
Definition of EXAFS
- Edge Step
- Energy to wave number
Fourier Transform (FT) of (k)
- FT is a frequency filter
- Different parts of a FT and backward FT
- FT windows and sills
- Determining Kmin and Kmax of FT
IFEFFIT method for constructing the background function
- FT and background (bkg) function
- Wavelength of bkg
EXAFS Equation
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File Number
(E)
=
(E) -
0
(E)
(E)
Definition of EXAFS
Measured Absorption
coefficient
Evaluated at the Edge step (E
0
)
~
(E) -
0
(E)
(E
0
)
Bkg: Absorption coefficient without
contribution from neighboring atoms
(Calculated)
Normalized
oscillatory part
of absorption
coefficient
=>
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Pre-edge region 300 to 50 eV before the edge
Edge region the rise in the absorption coefficient
Post-edge region 50 to 1000 eV after the edge
Absorption coefficient
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Edge step
Pre-edge line 200 to 50 eV before the edge
Post-edge line 100 to 1000 eV after the edge
Edge step the change in the absorption coefficient at the edge
- Evaluated by taking the difference of the pre-edge and
post-edge lines at E
0
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Athena normalization parameters
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File Number
k
2
= 2 m
e
(E E
0
)

Energy to wave number

E
0
Must be
somewhere
on the edge
Mass of the
electron
Planks
constant
Edge
Energy
~ E
3.81
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File Number
Athena edge energy E0
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File Number
FT of Sin(2Rk) is a peak at R=1
FT of infinite sine wave is a delta function
Signal that is de-localized in k-space is localized in R-space
FT is a frequency filter
Fourier Transform is a frequency filter
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Fourier Transform of a function that is:
De-localized in k-space localized in R-space
Localized in k-space de-localized in R-space
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The signal of a discrete sine wave is the sum of an infinite sine wave
and a step function.
FT of a discrete sine wave is a distorted peak.
EXAFS data is a sum of discrete sine waves.
Solution for finite data set is to multiply the data with a window.
Fourier Transform is a frequency filter
Regularly spaced ripple
Indicates a problem
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Fourier Transform
Multiplying the discrete sine wave by a window
that gradually increases the amplitude of the
data smoothes the FT of the data.
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File Number
Fourier Transform Windows
dk
k
min
k
max
dk
Welch
Parzen
Sine
Kaiser-Bessel
Hanning
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File Number
Athena plotting in R-space
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Parts of the Fourier transform
The Magnitude of the Fourier transform does not contain as
much information as the Real or Imaginary parts of the FT.
0 2 4 6 8
-0.8
-0.4
0.0
0.4
0.8
0 2 4 6 8 10 12
-0.8
-0.4
0.0
0.4
0.8
0 2 4 6 8
-0.8
-0.4
0.0
0.4
0 2 4 6 8
0.0
0.2
0.4
0.6
0.8
0 2 4 6 8 10 12
-0.8
-0.6
-0.4
-0.2
0.0
0.2
0.4
0.6
0.8
0 2 4 6 8
-0.8
-0.4
0.0
0.4
0.8
R
e
(
F
T
(

(
k
)

k
3
)
)

(

-
4
)

R ()
k (
-1
)

(
k
)

k
2

(

-
2
)

R ()
I
m
(
F
T
(

(
k
)

k
2
)
)

(

-
3
)
|
F
T
(

(
k
)

k
2
)
|

(

-
3
)
R ()
k (
-1
)
|

(
q
)
|

a
n
d

(
k
)
k
2

(

-
2
)
P
a
r
t
s

o
f

F
T
(

(
k
)

k
2
)

(

-
3
)
R ()
Real part of FT (k)
= Re [(R)]
magnitude of FT (k) = |(R)|
Imaginary part of FT (k)
= Im [(R)]
(k) data and FT window
back FT of (R) = (q)
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File Number
Backward Fourier transform
Only the wavelengths that are contained in the back Fourier
transform R range are present in the Re[chi(q)] spectra
As a larger R range is included the back FT looks more like the
original spectra (blue symbols)
0 1 2 3 4 5 6
0.0
0.2
0.4
0.6
0.8
1.0
1.2
|
F
T
(

(
k
)

k
2
)
|

(

-
3
)
R ()
0 2 4 6 8 10 12 14
-0.75
0.00
0.75
1.50
2.25
3.00
k (
-1
)
R
e
[

(
q
)
]

a
n
d

(
k
)
k
2

(

-
2
)
4
3
2
1
4
3
2
1
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File Number
How to Choose Minimum K of FT
Choose Kmin in the region where the background
doesnt change rapidly.
- Often around 2 to 4
-1
- Vary E
0
and plot the resulting spectra with low k-weight to
determine the best value.
0 2 4 6 8 10 12
-0.4
-0.2
0.0
0.2
0.4
17150 17200 17250
0.0
0.1
0.2
0.3
0.4
0.5
0.6
0.7
0.8
0.9
1.0
k (
-1
)

(
k
)

k

(

-
1
)

(
E
)

x
Incident x-ray energy (eV)
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File Number
Choosing Maximum K-range
The FT should be smooth and free of ringing
To choose Kmax make vary the kmax value and plot
the data using the largest k-weight that will be used
in modeling
Look for ringing in the real or imaginary part of FT
In the example above kmax of 10 or 11
-1
best
0 2 4 6
-4
-2
0
2
4
0 2 4 6
-4
-2
0
2
4
0 2 4 6 8 10 12
-0.15
-0.10
-0.05
0.00
0.05
0.10
0.15
kmax = 8
-1
kmax = 9
-1
kmax = 10
-1
R ()
R
e

[
F
T
(

(
k
)

k
1
)
]

(

-
2
)
kmax = 10
-1
kmax = 11
-1
kmax = 12
-1
R
e

[
F
T
(

(
k
)

k
1
)
]

(

-
2
)
R ()

(
k
)

k
2

(

-
2
)

k (
-1
)
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File Number
Effect of K-weight on FT
These spectra have been k-weighted by 1, 2, and 3
and then rescaled so that the first peak in the FT are
the same height
The higher k-weight values give more importance to
the data above 6
-1
, this emphasizes the signal due
to the P neighbor relative to the O in the first shell
0 2 4 6
0
5
10
15
0 2 4 6
-10
-5
0
5
10
15
0 2 4 6 8 10 12 14
-20
-10
0
10
20
R ()
|
F
T
(

(
k
)

k
x
)
|

(

-
x
-
1
)
R
e

(
F
T
(

(
k
)

k
x
)
)

(

-
x
-
1
)
R ()
k (
-1
)

(
k
)
.
k
k
w

(

-
1
-
k
w
)
Kw=1
Kw=2
Kw=3
O
P
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File Number
Fourier transform parameters in Athena
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File Number
Background function overview
A good background function removes long wavelength
oscillations from (k).
Constrain background so that it cannot contain oscillations
that are part of the data.
Long wavelength oscillations in (k) will appear as peaks in
FT at low R-values
FT is a frequency filter use it to separate the data from
the background!
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File Number
Separating the background function from the data
using Fourier transform
Min. distance between
knots defines minimum
wavelength of background
Rbkg
Background function is made up of knots connected by 3
rd
order
splines.
Distance between knots is limited restricting background from
containing wavelengths that are part of the data.
The number of knots are calculated from the value for Rbkg and the
data range in k-space.
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File Number
Rbkg value in Athena
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File Number
How to choose Rbkg value
An example where background distorts the first shell peak.
R
bkg
should be about half the R value for the first peak.
R
bkg
= 2.2
R
bkg
= 1.0
A Hint that Rbkg may be too large.
Data should be smooth, not pinched!
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File Number
FT and Background function
R
bkg
= 1.0 R
bkg
= 0.1
An example where long wavelength oscillations appear
as (false) peak in the FT
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File Number
Frequency of Background function
Constrain background so that it cannot contain
wavelengths that are part of the data.
Use information theory, number of knots = 2 R
bkg
k /
8 knots in bkg using R
bkg
=1.0 and k = 14.0
Background may contain only longer wavelengths.
Therefore knots are not constrained.
Data contains this and
shorter wavelengths
Bkg contains this and
longer wavelengths
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File Number
The EXAFS Equation
(N
i
S
0
2
)F
i
(k) exp(i(2kR
i
+
i
(k)) exp(-2
i
2
k
2
) exp(-2R
i
/(k))
kR
i
2

i
(k) = Im(
)
R
i
= R
0
+ R
k
2
= 2 m
e
(E-E
0
)/
Theoretically calculated values
F
i
(k) effective scattering amplitude

i
(k) effective scattering phase shift
(k) mean free path
Starting values
R
0
initial path length
Parameters often determined
from a fit to data
N
i
degeneracy of path
S
0
2
passive electron reduction factor

i
2
mean squared displacement of
half-path length
E
0
energy shift
R change in half-path length
(k) =
i

i
(k)
with
R
0
Photoelectron
Scattered
Photoelectron
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File Number
More Information
www.xafs.org
Kelly, S D, Hesterberg, D and Ravel, B. Analysis of soils and
minerals using X-ray absorption spectroscopy. In Methods of
soil analysis, Part 5 -Mineralogical methods; Ulery, A. L.,
Drees, L. R., Eds.; Soil Science Society of America: Madison,
WI, USA, 2008; pp 367.